Panicle Traits Research Articles

Local Taxonomy and Diversity of Chadian Sorghum [<i>Sorghum bicolor</i> (L.) Moench] Accessions

The integration of local plant genetic resources into the breeding program is an asset for research. The objective of this study is to assess the diversity and analyze the management practices of cultivated sorghum. A questionnaire following a participatory approach was submitted to 675 producers in 45 villages. The cultivars collected were characterized using 9 qualitative descriptors. In total, 151 accessions and 191 names were inventoried. On average, 25.17 accessions per department and 3.36 accessions per village. Local taxonomy is based on many criteria expressed in different local languages. The most common method of naming is that to the word sorghum is added either the color of the grain, the precocity, or any element deemed relevant by the farmers. Significant variability in grain and panicle traits was observed within the collection, except the color of the endosperm. The rate of diversity loss is 11.52% and red grain sorghums are the most threatened with extinction. Five accessions groups are differentiated by the presence or absence of awns, the color of glumes, and amount of grain covered by glumes, grain plumpness, and form. Based on productivity, precocity, plant size, seed shape, and color, the farmers identified seven promising accessions. This potential will be preserved and developed in the sorghum varietal improvement program in Chad.

Genetic variability of panicle architecture in indigenous rice landraces of Koraput region of Eastern Ghats of India for crop improvement.

Panicle architecture is an important character that influence reproductive success and contributes directly to grain yield. In the present study, we evaluated diversity of panicle traits in 77 indigenous rice landraces from Koraput and compared with three popularity cultivated hybrid varieties of the locality for possibility of using in crop improvement program. Significant morphological variations of panicle traits such as panicle number, panicle angle, panicle weight, panicle length, grain number and grain weight were recorded in studied rice landraces. Based on the principal component analysis, first two axis of principal component captures 56.34% of the total variation and indicated significant variability of panicle traits among the genotypes. Panicle length, panicle weight, grain number and flag leaf area are the major determinants of phenotypic diversity. Multiple correlation between traits indicated that panicle weight in studied rice landraces were positively correlated with panicle number, grain number and leaf area and negatively associated with panicle length, panicle angle and chaff number. The genetic advance as percentage of mean (GAM) ranged from 22.19% for panicle length to 147.02% for panicle angle. High GAM along with heritability was observed for panicle number, panicle weight, grain number and chaff number and are important traits for selection during crop improvement. Some of the landraces such as Matidhan, Bhatagurumukhi, Chiklakoli and Kamuntana remarkably showed superior panicle weight along with higher grain number and length of panicle, which can be used in the future rice breeding program.

Yield characteristics of japonica/indica hybrids rice in the middle and lower reaches of the Yangtze River in China

Although a lot of researches have been done on yield characteristics of japonica/indica hybrid rice, there is little information on differences of yield characteristics between different types of hybrid. To determine common characteristics of japonica/indica hybrid rice (JIHR) and identify the differences between different types of JIHR, the present study assessed yield characteristics, such as panicle trait, leaf area index (LAI), above-ground biomass accumulation, and nitrogen absorption and utilization, among three types of cultivar of JIHR. In our field experiments, three types of JIHR, e.g., Yongyou, Chunyou and Jiayouzhongke, were divided, and each of them has two cultivars, which were used as materials, meanwhile, using conventional japonica rice (CJR) Wuyingjing 31 and Sujing 9 were as controls. The results showed that the mean yield of those JIHR was above 12 t ha−1 in 2017 and 2018, and was 31.9 and 32.2%, respectively higher than that of CJR in the two years. Spikelet number per panicle of JIHR resulted in high yield. Higher yield of JIHR was likely contributed to greater panicle number and more spikelets per panicle. Higher yielding JIHR showed stronger tillering capacity, larger LAI and above-ground biomass accumulation from jointing to heading stages, which likely contributed to the higher number of spikelets per panicle. The long duration from heading to maturity stages allowed more nitrogen accumulation of higher yielding JIHR.

SNP-based QTL mapping for panicle traits in the japonica super rice cultivar Liaoxing 1

Panicle traits directly associated with yield are a target of selection in rice breeding. Although abundant QTL for panicle traits have been identified, there is little information about the genetic basis of panicle traits in japonica super rice (JSR) cultivars. In this study, we identified QTL for panicle traits in three environments using a population of recombinant inbred lines (RILs) derived from the JSR cultivar Liaoxing 1. A total of 197 RILs were genotyped with 285 polymorphic SNP markers. Phenotypic data and best linear unbiased prediction (BLUP) value of primary branch number (BNP), secondary branch number (BNS), grain number on primary branch (GNP), grain number on secondary branch (GNS), grain number per panicle (GN), panicle length (PL) and grain density (GD) were used for QTL mapping. A total of 105 QTL for seven panicle traits were detected in single environments using their BLUP values. Individual QTL explained 0.51%–52.22% of the phenotypic variation. Of the 105, 49 were also detected by joint multi-environment analyses. Five stable QTL: qGD9, qPL9, qGNP9, qGN6, and qBNS6.2 were identified in multiple environments. qGD9, qGNP9, and qPL9, co-localizing on chromosome 9, likely correspond to the known gene DEP1. Importantly, qGN6 and qBNS6.2 in a co-localization region were identified as novel QTL, and their Liaoxing 1 alleles had a positive effect. Several RILs with the QTL allele combinations qGD9/qPL9/qGNP9 and qGN6/qBNS6.2 showed greater GN. Further investigation of the putative gene underlying qGN6/qBNS6.2 would shed light on the molecular mechanism of JSR.

Genetic diversity of panicle morphological traits of rice (Oryza sativa L.)

The variability of rice genotypes is a source of germplasm for rice breeding. As one of the major organs related to yield components in rice, panicle architecture is an important part to be studied, while the information is still limited. The study aimed to obtain information on the diversity of rice genotypes on the panicle character and investigate their relationship within the panicle characters. The experiment was conducted during two seasons using 100 rice genotypes. The analysis of variance showed that genotypes and seasons are significantly different. The character of length of first grain from first node and the number of primary branches increased during the rainy season (rainy season 2015/2016). The performance of panicle traits had been influenced by environment factors regarding to quantitative traits which encoded by multiple genes.

Impact of sorghum racial structure and diversity on genomic prediction of grain yield components

AbstractPopulation structure is an important factor that affects the accuracy of estimated breeding values in genomic prediction. Natural sorghum [Sorghum bicolor (L.) Moench] populations exhibit population structure resulting from genetic and morphological differentiation due to evolutionary divergence. To study the impact of sorghum racial structure and diversity in genomic prediction, we conducted two cross‐validation (CV) experiments: CV1, proportional sampling from races; and CV2, sampling from across race (AR) or within race (WR). A diversity panel with 389 individuals with 224,007 single nucleotide polymorphisms was used for genomic prediction. Genomic heritabilities for traits were positively correlated (0.63) with their mean prediction accuracy (r) from CV1, and within‐subpopulation variance accounted for ∼80% of total genetic variance. The CV1 prediction accuracy ranged from 0.52–0.69, but r declined by 39 and 54% on average for WR and AR methods, respectively. As a predictor, race explained 30–50% of covariance for grain and panicle traits, but race was a bad predictor of plant height, as expected. Grain weight was consistently the best predicted trait across CV1 and CV2 methods except in AR. Difference in average r for WR and AR was greater in durra and caudatum, small in kafir, and nonexistent in guinea and mixed subgroups. We observed higher prevalence of minor alleles among guinea and mixed subgroups, highlighting contribution of allelic diversity towards prediction accuracy. Genomic prediction in sorghum will benefit from utilization of interracial diversity, and we emphasize the need for further investigations into the role of racial structure in genomic prediction.

A method for characterizing the panicle traits in rice based on 3D micro-focus X-ray computed tomography

Characterizing panicle traits is essential for measuring rice production. Because these traits can be used to analyze the effects of different genes on the rice. The spikelet number and the seed setting rate are usually considered to be more crucial. In existing characterizing methods, each grain of the panicle must be spread out manually to reduce the overlapping areas and made existing 2D imaging for the unfolded panicle. However, these methods, which maybe influence the panicle structure, are inefficient and complicated for operating, and cannot determine the seed setting rate. For the problems mentioned above, X-ray CT, as a non-destructive technique, can be used to examine and characterize the internal structure of the panicle. Therefore, in this paper, the panicle was scanned and reconstructed by Microfocus CT System. The panicle traits were detected by combination of distance transform watershed algorithm and 3D connected domains. The effectiveness of this method was verified by accuracy calculation of eight different rice panicle samples. This method is of great significance in practical application.

Detection of QTL for panicle architecture in $$\hbox {F}_{2}$$ population of rice

Panicle traits are the most important agronomic characters which directly relate to yield in rice. Panicle length (PL) being one of the major components of rice panicle structure is controlled by quantitative trait loci (QTLs). In our research, conducted at Research Farm of SKUAST-J, crosses of parental lines K343 and DHMAS were made for generating F2 mapping population, which were then transplanted into the field using augmented design-I. The F2 population was used for phenotypic evaluation, development of linkage map and identification of QTLs on the chromosomes by using SSR markers. A total of 450 SSR markers were used for screening both the parents of which 53 highly polymorphic markers were selected and used for genotyping of 233 genotypes of F2population. Linkage map was generated using MAPMAKER/EXP3.0 software, seven linkage groups were found distributed on 11 chromosomes of rice. QTLs were detected using QTL Cartographer (v2.5) software. Based on 1000 permutation tests, a logarithm of odds (LOD) threshold value 2.0 and 3.0 was set. Composite interval mapping was used to map QTLs in populations derived from bi-parental crosses. The phenotypic data, genotypic data and the genetic linkage map generated identified total three QTLs of which one was identified for PL qPL2, located at 85.01 cM position with 2.1 LOD value and in between the marker intervals RM324-RM208, this QTL explained the phenotype variation by 4.36%. The other two QTLs were identified for spikelet density (SD) qSD3.1 and qSD3.2, located at 28.91 and 39.51 cM, respectively, both with a flanking marker RM6832 on chromosome 3. The LOD value and phenotypic variation explained for qSD3.1 and qSD3.2 was 3.00 and 3.25; 9.70 and 12.34% respectively. The reported QTLs identified in the study suggested a less diversity in the parents used and also the rejection of not so useful markers from the used set of markers for PL and SD.

Mapping quantitative trait loci and meta-analysis for cold tolerance in rice at booting stage

Low temperature at the booting stage is a major abiotic stress-limiting rice production. In this study, Cold stress tolerance index of panicle traits of a recombinant inbred line was used to identify cold tolerance at booting stage for three consecutive years. The purpose was to locate the stable QTL linked to cold tolerance at booting stage. Combined with meta-analysis model, candidate genes for cold tolerance were mined. The results showed that a total of 17 cold resistant QTLs were detected, of which 5 were pleiotropic interval (CTB2-1, CTB6-2, CTB7-1, CTB7-2 and CTB7-4). However, only three traits obtained the same QTLs in different years, which indicated that cold tolerant QTL at the booting stage was greatly affected by environment. The six selected progenys with cold tolerance alleles can be used in cross combinations. A total of 47 cold tolerance meta-QTLs (MCqtl) were obtained from the meta-analysis, of which 8 reported cold response genes were found in 7 MCqtl regions, and 18 candidate genes conferring cold tolerance were identified, of which 10 candidate genes showed hits to ESTs expressed in the reproductive tissue. These results would lay a foundation for fine mapping of QTLs/genes related to cold tolerance in booting stage and marker-assisted selection for breeding in rice.

Quantitative trait loci mapping of panicle traits in rice.

In this study 90 individuals of recombinant inbred lines (RILs) were developed by crossing subspecies of japonica rice cultivar, ‘Nagdong’ and an indica type cultivar, ‘Cheongcheong’. These individuals were used to identify the quantitative trait loci of panicle traits using SSR markers. A genetic linkage map was constructed using one hundred fifty four simple sequence repeat (SSR) primers covering distance of 1973.6 cM of the whole genome with mean distance of 13.9 cM among markers. QTLs were mapped using composite interval mapping method, nineteen QTLs were recognized for the panicle traits on chromosomes 4, 5, 6, 8, 10, 11, 12 with individual QTL explained 8.8% to 37.9% of phenotypic variation. Two pleiotropic effects loci were found on chromosomes 4 and 6. These QTLs affecting leaf traits, panicle traits and panicle branch traits would be beneficial to high-yield rice improvement.

Locating QTL associated with spike traits of Dongxiang wild rice (Oryza rufipogon Griff.)

Improvements in the spike of rice play an essential role in modern super-rice breeding projects. In this study, two sets of population, including 230 F2 plants and 150 F2:3 lines derived from a cross of Dongxiang wild rice (DXWR) and 93–11, were developed to identify quantitative trait loci (QTLs) for spike traits. A total of 38 QTLs affecting 20 spike traits and 37 epistatic QTL pairs with more than one interaction were detected in the two populations, explaining the wide phenotypic variation of QTLs ranging from 10.17 to 47.79% and from 27.07 to 78.60%, respectively. Among these QTLs, eight genomic regions containing clustered QTLs affecting two or more traits were detected on chromosome 3, 6, 7, 8, and 12 in the two populations, and two co-localized QTLs were located at intervals of RM3724–RM5745 and RM3484–RM6776 on chromosome 6 and 7, with pleiotropic effects on the MPW, NPB, GSD, NFG, and PpbIVIL. The additive-dominant-epistatic QTLs played an essential role in controlling the genetic expression of panicle traits in DXWR. Overall, these results can serve as a foundation for facilitating future cloning and molecular breeding in crop science.

Novel Imaging Techniques to Analyze Panicle Architecture.

Panicle architecture is known to directly influence grain yield in rice, and thus is an important trait for rice varietal improvement. However, spike branching consequences trigger variation in number of superior and inferior grains and thus affect grain quality. The genetics behind the length of both primary and secondary branches were studied resulting in the identification of cloned genes. Extending this knowledge to include other physiological parameters of panicle architecture is not yet well studied, and it requires high-throughput imaging techniques that are accurate. In this chapter we put the spotlight on Panicle Trait Phenotyping Tool (P-TRAP), a freely available platform independent software to analyze the panicle architecture of rice, as one of such methods that can be used to generate a comprehensive and reproducible panicle architecture data and identify superior breedinglines. P-TRAP measures 15 panicle structure and nine spikelet traits. These quantitative traits can be used in genome-wide association studies to understand their genetic basis.

Learning from farmers to improve sorghum breeding objectives and adoption in Mali

ABSTRACT Many efforts have been made to improve sorghum [Sorghum bicolor (L.) Moench] varieties, but adoption of improved varieties remains low. Sorghum has diverse panicle architecture and grain qualities that vary within and between races, and utilization and adoption may depend on these traits. Recent efforts in West Africa to improve local guinea race germplasm as a base material have diversified potential options: there are breeding materials with a range of panicle types with increased grain number per panicle and a range of droopiness, as well as laxness and threshability. This study was designed to expand our understanding about sorghum grain and panicle traits that are important for farmers in the Sudan savanna zone of Mali. We combined a sorghum panicle sorting activity with qualitative interviews in Mande and Dioïla to understand farmers’ knowledge and preferences about sorghum characteristics. A total of 20 panicle sorting activities and 20 interviews were conducted with men and women sorghum producers. Based on their roles and responsibilities in sorghum production and processing, farmers associated specific panicle types, plant types, and grain traits with aspects of pest control, threshability, storage duration, and yield. Farmers preferred open panicles and droopy architecture for disease and pest control; hard grains for storage and appropriate ratios of flour and grits; high density of grain on the panicle for yield; and specific glume qualities for threshability. Breeding programs need to consider these regional preferences and gender roles to develop appropriate material and increase adoption of productive varieties.

Relationships between different morphological traits of panicles and seeds of Dactylis glomerata L. varieties

This study was aimed to evaluate morphological characteristics of the panicle as well as seeds of Dactylis glomerata varieties relevant for the assessment of seed production. Six varieties different in earliness were sown in two row spacing. Panicle traits: length, number of the 1st and the 2nd order branches as well as 1000-seed weight and morphological seed traits were assessed during 4-year utilization. Significant differences between varieties were found according to the panicle length, number of the branches and 1000-seed weight depending on the year of utilization as well as with reference to evaluated seed traits, irrespectively on year and row spacing. The results showed that the main traits determining the seed weight per panicle of Dactylis glomerata varieties are the panicle length and the number of the 1st order branches. Whereas, seed morphological traits had impact on 1000-seed weight and seed weight per panicle only in the second year of use, in which the highest rainfall than in the other years and moderate temperatures were recorded.

Morfologi Malai Padi (Oryza sativa L.) pada Beragam Aplikasi Pupuk Nitrogen

<p align="center"><strong><em>ABSTRACT</em></strong></p>The effects of nitrogen fertilizer on agronomic and morphological characters depend on several factors such as genotypes and nitrogen rate. The study was aimed to evaluate nitrogen effects on rice panicle. A field experiment was conducted at Babakan Research Station during November 2015- February 2016 using a split-split plot design with three replicates. Nitrogen doses was a main plot, genotypes was a subplot, and time of application was a sub-subplot. A greenhouse experiment was carried out at PAIR, Jakarta during February-July 2017 using a completely randomized design with three replicates. The results from the field experiment indicated that the highest panicle number (13.25), number of filled grains (177.94) and spikelet number (213.76) were obtained at doses of 450 kg urea ha-1. Analysis of variance showed that the genotypic effects were significant for all traits observed, while the interaction effect between genotypes and time of nitrogen application was significant on the length of first grain from first node. However, the three-factors interactions were not significant for all traits. The greenhouse experiment revealed that both genotypes and N rates significantly affected all traits except for panicle number and the length of first grain from first node, respectively, while their interaction only significant for number of primary branch. Nitrogen increased all traits observed except the length of first grain from first node. Simultaneously, both experiments showed significant effects of genotypes for all traits observed. Doses of urea fertilizers above 400 kg ha-1 could improve the performance of panicle traits in order to increase yield potential.<br /><br />Keywords: length of first grain from first node, number of primary branches, panicle length, panicle number

Overexpression of RCc3 improves root system architecture and enhances salt tolerance in rice

Root system architecture represents an underexplored target for improving global crop yields. In this study, we investigated the biological role of the rice root–specific gene RCc3 in improving root growth and responses to abiotic stress by overexpressing RCc3 in rice plants. RCc3 was induced by osmotic and heat stress. RCc3 overexpression produced pleiotropic phenotypes of improved root system architecture, including increased growth of primary root, adventitious roots and lateral roots at the seedling stage. Further study indicated that auxin accumulation in the root was increased through auxin local biosynthesis and polar auxin transport in RCc3 overexpression lines. At maturity, the plant height and panicle traits were also significantly enhanced in overexpression plants. Under osmotic and heat stress conditions, the root and shoot growth were less severely inhibited in RCc3 overexpressing transgenic plants than that in wild–type plants, and the transcript levels of abiotic stress–related genes were significantly increased. Moreover, overexpression of RCc3 remarkably enhanced the tolerance to salt stress, with the elevated activities of antioxidant enzymes. Taken together, the data showed that RCc3 overexpression can improve rice root system, promote plant growth, and enhance plant tolerance to salt stress.

Development and Utilization of Introgression Lines Using Synthetic Octaploid Wheat (Aegilops tauschii × Hexaploid Wheat) as Donor

As the diploid progenitor of common wheat, Aegilops tauschii Cosson (DD, 2n = 2x = 14) is considered to be a promising genetic resource for the improvement of common wheat. In this work, we demonstrated that the efficiency of transferring A. tauschii segments to common wheat was clearly improved through the use of synthetic octaploid wheat (AABBDDDD, 2n = 8x = 56) as a “bridge.” The synthetic octaploid was obtained by chromosome doubling of hybrid F1 (A. tauschii T015 × common wheat Zhoumai 18). A set of introgression lines (BC1F8) containing 6016 A. tauschii segments was developed and displayed significant phenotype variance among lines. Twelve agronomic traits, including growth duration, panicle traits, grain traits, and plant height (PH), were evaluated. And transgressive segregation was identified in partial lines. Additionally, better agronomic traits could be observed in some lines, compared to the recurrent parent Zhoumai 18. To verify that the significant variance of those agronomic traits was supposedly controlled by A. tauschii segments, 14 quantitative trait loci (QTLs) for three important agronomic traits (thousand kernel weight, spike length, and PH) were further located in the two environments (Huixian and Zhongmou), indicating the introgression of favorable alleles from A. tauschii into common wheat. This study provides an ameliorated strategy to improve common wheat utilizing a single A. tauschii genome.

Analisis Genetik Arsitektur Malai Padi Menggunakan Dua Populasi F2

<em>Improvement of rice panicle architecture is one important objective in the development of improved new-plant-type rice varieties. Panicle architecture is directly related to yield components in rice. The aims of this study were to obtain information on inheritance pattern of panicle architecture on F2 generation and to obtain the best selected individuals. The experiment was conducted at Sawah Baru Experimental Farm Bogor, from May to October 2016. Two F2 populations derived from crosses of IPB 3S/IPB160-F-36, IPB160-F-36/IPB 5R and three genotypes of parents were used as experimental materials. A total of 208 and 204 plant samples were taken representing each of the two F2 populations and 20 plants representing the parents. Three panicles were taken randomly from each individual as observed samples. The results showed that additive gene action influenced number of primary branches in population of IPB 3S/IPB160-F-36, whereas in the population of IPB160-F-36/IPB 5R, most of the panicle architecture traits were controlled by additive gene action except for the length of primary branches. All of panicle architecture traits were controlled by relatively many genes except length of primary branches and number of grains on primary branches in the IPB 3S/IPB160-F-36 population. The panicle architecture of the two observed population was genetically varies. The heritability estimates were moderate to high. Selection could increase the mean of panicle architecture traits using either single or multiple traits simultaneously.<br /><br />Keywords: gene action, heritability, genetic variability, panicle traits <br /><br /></em>

Dissecting the genetic basis of heavy panicle hybrid rice uncovered Gn1a and GS3 as key genes.

Shuhui498 (R498) is an elite parent of heavy panicle hybrid rice by pyramiding the rare gn1a and null gs3 alleles. This finding reveals the genetic basis and great potential application in future breeding of R498. The heavy panicle trait, defined as 5g or more of grain weight per panicle, is one of the target traits in super-high-yield rice breeding programs. The use of heavy panicle-type hybrid rice has been shown to be a successful strategy for super-high-yield breeding programs, particularly under the environmental conditions of high humidity and deficient solar radiation in southwestern China. However, the genetic components of the heavy panicle trait in hybrid rice remain elusive. Here, we report that the combination of loss-of-function mutations in Grain number 1a (Gn1a) and Grain Size 3 (GS3) is responsible for the heavy panicle phenotype of the elite hybrid rice restorer line Shuhui498 (R498). The null gn1a allele is the determinant factor for heavy panicles through increased grain number, while gs3 is associated with grain size and weight. R498 pyramided the two major null alleles, resulting in heavy panicles with a high grain number and large grains. Clustering analysis revealed that the null gn1aR498 allele is a rare haplotype which has been innovatively utilized in R498, underscoring the great potential of R498 for breeding purposes. Our research thus sheds light on the distinct genetic compositions of heavy panicle-type rice and may potentially facilitate super-high-yield rice breeding.

Introgression of a functional epigenetic OsSPL14WFP allele into elite indica rice genomes greatly improved panicle traits and grain yield

Rice yield potential has been stagnant since the Green Revolution in the late 1960s, especially in tropical rice cultivars. We evaluated the effect of two major genes that regulate grain number, Gn1a/OsCKX2 and IPA1/WFP/OsSPL14, in elite indica cultivar backgrounds. The yield-positive Gn1a-type 3 and OsSPL14WFP alleles were introgressed respectively through marker-assisted selection (MAS). The grain numbers per panicle (GNPP) were compared between the recipient allele and the donor allele groups using segregating plants in BC3F2 and BC3F3 generations. There was no significant difference in GNPP between the two Gn1a alleles, suggesting that the Gn1a-type 3 allele was not effective in indica cultivars. However, the OsSPL14WFP allele dramatically increased GNPP by 10.6–59.3% in all four different backgrounds across cropping seasons and generations, indicating that this allele provides strong genetic gain to elite indica cultivars. Eventually, five high-yielding breeding lines were bred using the OsSPL14WFP allele by MAS with a conventional breeding approach that showed increased grain yield by 28.4–83.5% (7.87–12.89 t/ha) vis-à-vis the recipient cultivars and exhibited higher yield (~64.7%) than the top-yielding check cultivar, IRRI 156 (7.82 t/ha). We demonstrated a strong possibility to increase the genetic yield potential of indica rice varieties through allele mining and its application.