Double-cross Populations Research Articles

The selection index of S3 corn convergent breeding population based on multivariate analysis

Abstract. Makmur, Farid M, Ala A, Mandja K, Anshori MF, Fadhilah AN. 2024. The selection index of S3 corn convergent breeding population based on multivariate analysis. Biodiversitas 25: 1097-1103. Corn is one of the most important and strategic food crops in the world, including Indonesia. Increasing corn production through a plant breeding program by assembling hybrid varieties begins with developing a convergent breeding population and index selection. The research aims to identify genetic variance and the effectiveness of selection indices in selecting high-yield S3 cross populations. The research was carried out in Rea Village, Binuang Sub-District, Polewali Mandar District, West Sulawesi from July to November 2022. The research used an augmented design with four blocks. Sixty-six lines were derived from 4 double cross populations and 8 populations of the S3 generation multiple-cross population, as well as 9 check varieties (NK7328, Pioneer 36, Bisi 18, Bisi 2, NK99, Nasa 29, JH45, Bisi 9, and NK212) were used in this study. The results indicate that the length of cobs (5.98;73.59%), length of seed cobs (7.06; 79.46%), weight of 100 seeds (7.75; 89.30%), and weight of seeds per cob (7.84; 65.59%) have moderate genetic variance and high heritability. The characteristics of stem diameter, yield percentage, and weight of seed per cob were effectively used in the selection index formulation. Based on the index selection, there were 14 potential corn lines with a good performance, recommended for the next hybridization stage.

Selection criteria and index analysis for the S2 maize lines of double-crosses

Abstract. Akfindarwan AK, Farid M, Syaiful SA, Anshori MF, Nur A. 2023. Selection criteria and index analysis for the S2 maize lines of double-crosses. Biodiversitas 24: 192-199. This study aimed to determine the selection criteria and the selection index for the S2 maize lineage from double cross crosses and to select the potential lines that could be continued in the S3 generation. The research was carried out in the field from July to November 2020 at the Experimental Farm of the Agriculture Faculty, Hasanuddin University, Tamalanrea District, Makassar City, South Sulawesi. The maize lines used were derived from 4 double cross populations of S1 generation, namely: DC1 (P36/B9//NK7328/JH2) with 19 genotypes, DC2 (B9)/HJ28/NK728), DC3 (B18/B2/B2/N29), and DC4 (JH45/B19/N29/B2). The results of this study revealed that the selection criteria suitable for this population were the weight of seeds per cob, peel cob weight, and weight of 100 seeds. Furthermore, the selection index analysis showed that there were 61 promising lines for F2 double cross maize that had a positive index value, while based on the Z value, there were 44 lines that had a better index value than the best parents. Therefore, it is recommended that the 61 S2 Maize lines from double crosses be further tested on to the S3 generation.

Selection of tomato breeding lines based on morphological traits associated with high yield potential in double-cross population

Abstract. Anisa WN, Afifah EN, Murti RH. 2022. Selection of tomato breeding lines based on morphological traits associated with high yield potential in double-cross population. Biodiversitas 23: 2973-2980. Low tomato production is a global problem. Plant breeding has been intensified to develop high-yield varieties and meet the high production of vegetable crops. Selection is an essential part of plant breeding to evaluate desirable traits of breeding lines. This study aimed to identify tomato breeding lines with high yield potential from 13 breeding lines and 2 commercial tomatoes. Collected data were analyzed using analysis of variance, post hoc, path, and principal component analysis. Results showed that 9 tomato lines, namely, BV-1, BV-2, BV-3, BV-6, BV-7, BV-9, BV-11, BV-12, and BV-13 had a high yield potential based on the number of fruits per plant and fruit weight. Given their high path coefficient value and significant correlation (P<0.05) with the yield potential, these two characteristics are highly recommended to be used as selection criteria for the high yield potential of tomato plants. The following characteristics had a high value of heritability: fruit weight, fruit length, fruit diameter, fruit firmness, fruit locules, fruit pericarp thickness, total soluble solid, number of flowers per bunch, number of fruits per bunch, number of fruits per plant, and harvesting age.

Genome-wide identification of agronomically important genes in outcrossing crops using OutcrossSeq

Many important crops (e.g., tuber, root, and tree crops) are cross-pollinating. For these crops, no inbred lines are available for genetic study and breeding because they are self-incompatible, clonally propagated, or have a long generation time, making the identification of agronomically important genes difficult, particularly in crops with a complex autopolyploid genome. In this study, we developed a method, OutcrossSeq, for mapping agronomically important loci in outcrossing crops based on whole-genome low-coverage resequencing of a large genetic population, and designed three computation algorithms in OutcrossSeq for different types of outcrossing populations. We applied OutcrossSeq to a tuberous root crop (sweet potato, autopolyploid), a tree crop (walnut tree, highly heterozygous diploid), and hybrid crops (double-cross populations) to generate high-density genotype maps for the outcrossing populations, which enable precise identification of genomic loci underlying important agronomic traits. Candidate causative genes at these loci were detected based on functional clues. Taken together, our results indicate that OutcrossSeq is a robust and powerful method for identifying agronomically important genes in heterozygous species, including polyploids, in a cost-efficient way. The OutcrossSeq software and its instruction manual are available for downloading at www.xhhuanglab.cn/tool/OutcrossSeq.html.

Genetics of fertility restoration in the isocytoplasm allonuclear C-group of cytoplasmic male sterility in maize

Maize is one of the first crops to produce hybrids using cytoplasmic male sterile lines. The C-type cytoplasmic male sterile (CMS-C) line is vital for hybrid seed production, and the fertility-restoration reaction along with its stability has a direct bearing on its applications. However, fertility restoration mechanism of CMS-C is complex and is still not clear so far. To further explore the factors affecting the fertility restoration of maize CMS, a series of test crosses were carried out by pollinating the isocytoplasm allonuclear CMS-C lines C48-2, Chuangzaosi and C478 with the test lines 18 bai, zi 330, 5022 and the restorer line A619, respectively. Four F2 populations and six double-cross combinations were obtained from the self-cross of fertility restored F1 and pollinating male-sterility-maintained F1 with the male-fertility-restored F1, respectively. Meanwhile, we developed the incomplete diallel-cross combinations using the isocytoplasm allonuclear male sterile lines as maternal parents and their respective maintainer lines 48-2, huangzaosi and 478 as paternal parents. All the F1, F2 and double-cross populations were planted at distinct locations in different years, and the fertility-restoration reaction was scored by field investigation and pollen staining with I2-IK. The results were as follows: 1) The same test line could restore the CMS-C line at a certain genetic background, but failed to restore the CMS-C line at the other genetic backgrounds, suggesting that the genetic background of CMS-C lines plays an important role in the fertility restoration. 2) The fertile-to-sterile segregation ratio of (C48-2×A619) F2 population planted in both Sichuan and Yunnan fited well to 15:1 by the χ 2 test. However, the fertility level of individuals in Yunnan mainly belonged to the 3 and 4grades, but which in Sichuan mainly belonged to the 5 grade, indicating the environmental factors had effect on the fertility-restoration reaction of (C48-2×A619) F2. 3) In our study, 18 bai could not restore C478, and 48-2 could not restore C478, but the fertile and sterile segregated plants were unexpectedly found in their double-cross population [(C478×18 bai) F1S×(C48-2×18 bai) F1F]. The similar case was also observed in the double-cross population [(C48-2 × zi 330) F1S × (C478 × zi 330) F1F]. Therefore, we speculated that there are minor fertility restorer genes not only in the nuclear background of C48-2 and C478, but also in zi 330 and 18 bai, and when these minor genes were gathered by hybridization, they could restore the fertility of C478 and C48-2. This conforms to the restorer genes dose-effect for fertility restoration in the plant CMS system. These results not only contribute to our understanding of the complexity and diversity of CMS-C restoration mechanism, but also provide an important reference for the practical applications about maize CMS-C.

GACD: Integrated Software for Genetic Analysis in Clonal F1 and Double Cross Populations.

Clonal species are common among plants. Clonal F1 progenies are derived from the hybridization between 2 heterozygous clones. In self- and cross-pollinated species, double crosses can be made from 4 inbred lines. A clonal F1 population can be viewed as a double cross population when the linkage phase is determined. The software package GACD (Genetic Analysis of Clonal F1 and Double cross) is freely available public software, capable of building high-density linkage maps and mapping quantitative trait loci (QTL) in clonal F1 and double cross populations. Three functionalities are integrated in GACD version 1.0: binning of redundant markers (BIN); linkage map construction (CDM); and QTL mapping (CDQ). Output of BIN can be directly used as input of CDM. After adding the phenotypic data, the output of CDM can be used as input of CDQ. Thus, GACD acts as a pipeline for genetic analysis. GACD and example datasets are freely available from www.isbreeding.net.

Quantitative trait locus mapping with background control in genetic populations of clonal F1 and double cross.

In this study, we considered five categories of molecular markers in clonal F1 and double cross populations, based on the number of distinguishable alleles and the number of distinguishable genotypes at the marker locus. Using the completed linkage maps, incomplete and missing markers were imputed as fully informative markers in order to simplify the linkage mapping approaches of quantitative trait genes. Under the condition of fully informative markers, we demonstrated that dominance effect between the female and male parents in clonal F1 and double cross populations can cause the interactions between markers. We then developed an inclusive linear model that includes marker variables and marker interactions so as to completely control additive effects of the female and male parents, as well as the dominance effect between the female and male parents. The linear model was finally used for background control in inclusive composite interval mapping (ICIM) of quantitative trait locus (QTL). The efficiency of ICIM was demonstrated by extensive simulations and by comparisons with simple interval mapping, multiple‐QTL models and composite interval mapping. Finally, ICIM was applied in one actual double cross population to identify QTL on days to silking in maize.

Linkage analysis and map construction in genetic populations of clonal F1 and double cross.

In this study, we considered four categories of molecular markers based on the number of distinguishable alleles at the marker locus and the number of distinguishable genotypes in clonal F1 progenies. For two marker loci, there are nine scenarios that allow the estimation of female, male, and/or combined recombination frequencies. In a double cross population derived from four inbred lines, five categories of markers are classified and another five scenarios are present for recombination frequency estimation. Theoretical frequencies of identifiable genotypes were given for each scenario, from which the maximum likelihood estimates of one or more of the three recombination frequencies could be estimated. If there was no analytic solution, then Newton-Raphson method was used to acquire a numerical solution. We then proposed to use an algorithm in Traveling Salesman Problem to determine the marker order. Finally, we proposed a procedure to build the two haploids of the female parent and the two haploids of the male parent in clonal F1. Once the four haploids were built, clonal F1 hybrids could be exactly regarded as a double cross population. Efficiency of the proposed methods was demonstrated in simulated clonal F1 populations and one actual maize double cross. Extensive comparisons with software JoinMap4.1, OneMap, and R/qtl show that the methodology proposed in this article can build more accurate linkage maps in less time.

Breeding Investigations in Single and Double Cross F<sub>4</sub> and F<sub>5</sub> Populations of Bhendi [<i>Abelmoschus esculentus</i> (L.) Moench

A study was conducted to assess the genetic variability, correlation and path analysis in four single cross and three double cross F 4 and F 5 populations of bhendi. The study indicated that double cross populations have reported higher magnitude of variability compared to single cross populations. High variability was observed for number of fruits per plant, plant height, internodal length, fruit weight and fruit yield per plant. Moderate variability for fruit length and fruit diameter and low variability for days to first flowering, days to 50% flowering, number of seeds per fruit and 100-seed weight. Phenotypic correlation revealed high positive correlation of fruit yield per plant with number of fruits per plant, number of branches per plant, plant height, fruit weight, fruit length and 100-seed weight. Path analysis depicted high effect on number of fruits per plant, fruit weight, plant height and number of branches per plant with fruit yield per plant. To release importance of fruit yield, direct selection can be practiced for these characters.

Simultaneous selection for resistance to five bacterial, fungal, and viral diseases in three Andean × Middle American inter-gene pool common bean populations

Numerous bacterial, fungal, and viral diseases cause severe damage on roots, foliage, stem, pods, and seeds, resulting in yield and quality losses in common bean (Phaseolus vulgaris L.) worldwide. Cultivars with resistance to multiple diseases are needed to reduce these losses and dependence on pesticides for disease control. Our objective was to determine the effectiveness of simultaneous selection in the F1 and F2 for resistance to five diseases, namely angular leaf spot (ALS), anthracnose (ANT), bean common mosaic (BCM), common bacterial blight (CBB), and common bean rust (CBR) in three Andean x Middle American inter-gene pool double-cross populations, namely ST = ‘Chocho’/‘Catrachita’//G 5686/VAX 3, CN = ‘DIACOL Calima’/VAX 6//A 193/G 5686, and CB = A 483/‘Talash’//Wilkinson 2/G 5686. One hundred seventy-five F1 plants of ST, 177 of CN, and 195 of CB and their parents were evaluated in the greenhouse using sequential inoculations with pathogens causing BCM, CBR, ALS, CBB, and ANT, in that order. Progenies of surviving F1 plants were again evaluated in the F2, using similar sequential inoculations. The F4-derived F5 breeding lines were developed using single-seed descent method. No selection was practiced for any trait in the F3 and F4. In the F5, five breeding lines from ST, two from CN, and one from CB exhibited intermediate to high levels of resistance to the five diseases when compared with the parents. Thus, selection in the F1 and F2 was effective for simultaneous introgression of resistance to the five diseases in all three Andean × Middle American inter-gene pool common bean populations.

Gamete selection for improving physiological resistance to white mold in common bean

White mold (WM), caused by Sclerotinia sclerotiorum (Lib.) de Bary, is a widespread disease of dry and green bean (Phaseolus vulgaris L.) in North America. Gamete selection (GS) was effective to combine and pyramide resistant genes and quantitative trait loci (QTL) for common bacterial blight. Our objective was to determine the effectiveness of GS to introgress physiological resistance to white mold. Two inter-gene-pool double-cross populations were developed. Selection for WM resistance was practiced from F1 to F4. Thirteen selected F1:5 breeding lines of each population and their four parents were evaluated. Two separate inoculations were made on each plant 1 week apart using a cut-stem method. The WM reaction was scored at 16, 23, and 33 days post inoculation (DPI) using a scale from 1 (no disease) to 9 (severely diseased or dead). In F1, 52% of Pop I (USPT-WM-1/CORN 601//USPT-CBB-1/92BG-7) and 67% of Pop II (Chase/I9365-25//ABL 15/A 195) susceptible plants were discarded. In F4, only 1.2% of families from Pop I, and 0.9% for Pop II, survived the selection process. An average of 20.5% gain in WM resistance was obtained for both populations in F4. Four breeding lines of Pop I had significantly (P = 0.05) lower WM score (4.1–4.6) and four were equal (4.7–4.9) to the best WM-resistant parent 92BG-7 (4.9), while ten breeding lines of Pop II were equal (4.5–4.8) to the best WM-resistant parent A 195 (4.6). Thus, GS was effective for improving WM resistance in common bean.

Effect of irrigation, mating schemes and selection methods on nature of association of seed yield and its components in blackgram

Phenotypic correlation of seed yield and its component traits were studied in four selected irradiated F,M, population, two three way and one double cross populations of blackgram advanced through bulk, individual plant selection (IPS) and single pod descent (SPD) method. All the twenty one populations exhibited significant positive correlation of plant height, number of clusters and pods per plant with seed yield per plant except three populations of bulk and one population of IPS method for plant height. Irradiated population of single cross 4 for pod length, single cross 1, 3 and three way cross 1 for number of seeds per pod exhibited significant positive correlation with seed yield per plant irrespective of the methods of advancement. The nature of association between pod length in three way cross 1 and number of seeds per pod in double cross advanced through bulk method was changed from negative to positive in IPS and SPD methods. Among the three methods of selection, single pod descent method showed a stronger magnitude and higher number of significant correlation in all the seven populations under study as compared to bulk and IPS methods. Most of the traits under study including pod length and number of seeds per pod contributed towards seed yield per plant in single cross F, M,, three way and double cross populations.

Selection for drought resistance in early generations of common bean populations

Availability and use of high-yielding drought-resistant common bean (Phaseolus vulgaris L.) cultivars would reduce dependence on irrigation water and production costs, stabilize yield in drought-prone environments, and potentially increase profit margins for growers. Among various selection criteria, seed yield has been found to be the most effective to improve drought resistance in common bean. Our objective was to determine the effectiveness of selection for seed yield in drought-stressed (DS) and non-stressed (NS) environments in early generations of common bean populations under field conditions. One hundred thirty-four F2-derived F4 (F2:4) families from each of three double-cross populations (SX 12008, SX 12009, and SX 12010), four parents, and six checks were evaluated in replicated field trials in DS and NS environments at the Centro Internacional de Agricultura Tropical, Palmira, Colombia during the January to March growing season (1997A). The 30 highest yielding F2:5 families from each population and each environment, four parents, and two checks were again evaluated in replicated trials in their respective DS and NS environments during the June to August growing season (1997B). Three F5:7 lines from each of the four highest yielding F2:5 families from each population and each environment (a total of 72 lines), and nine parents involved in the three populations were evaluated in replicated trials in both DS and NS environments in 1998B and 1999B. Mean yieldof lines selected in the NS environment was significantly higher than the mean of parents in populations SX 12008 and SX 12010 when tested in the NS environment. In population SX 12009, lines selected in the DS environment had higher mean yield than their parents when tested in NS environment. The mean yields of lines selected in the DS and NS environments did not differ significantly when tested in the DS environment in any population. NS environment seed yields were positively correlated with DS yields, geometric mean yield (GM), percent reduction (PR) due to drought stress, and drought susceptibility index (DSI). In contrast, DS and GM yields were negatively correlated with PR and DSI, whereas the association between the latter two was positive. The 100 -seed weight was slightly reduced and mean maturity was accelerated by 2 to 4 d in DS versus NS environments. Considering the extra costs involved to test early generation selections for seed yield in DS environments, it does not appear to be advisable in common bean. Key words: Drought resistance in common bean, early generation yield test, F2-derived family selection, Phaseolus vulgaris, seed yield

Heritability and Phenotypic Variation of Tolerance to Phytophthora Root Rot of Soybean

The most destructive fungal disease of soybean [Glycine max (L.) Merr.] is Phytophthora root rot. The most common method of protecting soybean from Phytophthora root rot utilizes specific resistance genes, but continuous selection pressure exerted on the pathogen frequently causes resistance genes in soybean to become ineffective. Infected plants which exhibit tolerance often yield nearly as well as uninfected resistant plants and prevent the buildup of races capable of overcoming resistance genes. Experiments were initiated to obtain information concerning the genetics of tolerance to Phytophthora root rot. The objectives were to: (i) compare parent‐offspring regression, correlation, and realized heritability estimates of tolerance, (ii) compare heritability and phenotypic variation among single‐, three‐way, and double‐cross populations, and (iii) correlate non‐infected yields with tolerance and maturity. Ten F3:4 populations were screened for tolerance in the F3 and F4 generations by the inoculum layer method. Heritability estimates were low, ranging from 0.17 to −0.10 when obtained through parent‐offspring regression. These estimates were not separable from zero because of the magnitude of their standard errors. Parent‐offspring correlation estimates were larger than parent‐offspring regression estimates, and ranged from 0.43 to −0.19. Realized heritability was estimated by selecting the 20% highest and lowest tolerant lines within each population. These results were generally larger, ranging from 0.80 to −0.13, and suggested that relatively high tolerant lines may be identified through selection. The number of parents composing a population did not influence heritability or phenotypic variation within populations. Most correlations among yield, tolerance, and maturity were non‐significant. Tolerance levels within populations should not vary with maturity. The inoculum layer method may not be sensitive enough to allow accurate screening of germplasm with low tolerance levels.

Independent, Alternate, and Simultaneous Selection for Resistance to Anthracnose and Angular Leaf Spot and Effects on Seed Yield in Common Bean (Phaseolus vulgaris L.)

Two double-cross populations were used to evaluate the efficiency of independent, alternate, and simultaneous selection practiced from the F2 to F8 for resistance to anthracnose and angular leaf spot of common bean (Phaseolus vulgaris L.). Seven resistant and high-yielding lines were selected from each of the four environments used during this study. These lines and the seven parents involved in two populations were evaluated in an 8 × 8 lattice design with three replications in two cropping seasons. Pathogen inoculum was used to create the three test environments: anthracnose alone, angular leaf spot alone, and anthracnose and angular leaf spot together. All entries were also evaluated in a fourth, disease-free environment. Selection for resistance to anthracnose and angular leaf spot was effective in both populations. Mean disease scores of all selected lines for anthracnose were lower than that of angular leaf spot irrespective of selection environment. Among the three stress environments, yields were higher in the anthracnose environment. However, lines selected alternately for anthracnose and angular leaf spot were usually higher yielding, and the highest yielding line in both populations originated from this selection environment. The mean yield of selected lines was higher and the highest yielding line originated from the population involving a parent (G 1805) belonging to the Mexican highland race ‘Jalisco’. Positive association existed between seed yield of protected and pathogen-inoculated environments. No association was found between resistance to anthracnose and angular leaf spot.

A comparison of anther culture derived material with single seed descent lines in Brussels sprouts (Brassica oleracea var. gemmifera)

Qualitative and quantitative studies show that diploid plants produced by anther culture (AC) from a double cross population of Brussels sprouts have arisen from spontaneously doubled haploid cells. The mean performance and distribution of lines produced by AC is compared to an equivalent array of inbred lines produced by single seed descent (SSD). There was no evidence of any difference in vigour between the AC and SSD samples. The tests are sufficiently sensitive to establish (with a 90 per cent confidence) that any true difference between the means, for vigour related traits, must be less than 15 per cent of the mean performance of SSD material. Additional evidence identifies genetic segregation for stability to micro-environmental factors within both the AC and SSD lines.