Browsing by Subject "Quantitative Genetik"

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Factors influencing the accuracy of genomic prediction in plant breeding
(2017) Schopp, Pascal; Melchinger, Albrecht E.
Genomic prediction (GP) is a novel statistical tool to estimate breeding values of selection candidates without the necessity to evaluate them phenotypically. The method calibrates a prediction model based on data of phenotyped individuals that were also genotyped with genome-wide molecular markers. The renunciation of an explicit identification of causal polymorphisms in the DNA sequence allows GP to explain significantly larger amounts of the genetic variance of complex traits than previous mapping-based approaches employed for marker-assisted selection. For these reasons, GP rapidly revolutionized dairy cattle breeding, where the method was originally developed and first implemented. By comparison, plant breeding is characterized by often intensively structured populations and more restricted resources routinely available for model calibration. This thesis addresses important issues related to these peculiarities to further promote an efficient integration of GP into plant breeding.
Optimum schemes for hybrid maize breeding with doubled haploids
(2011) Wegenast, Thilo; Melchinger, Albrecht E.
In hybrid maize breeding, the doubled haploid technique is increasingly replacing conventional recurrent selfing for the development of new lines. In addition, novel statistical methods have become available as a result of enhanced computing facilities. This has opened up many avenues to develop more efficient breeding schemes and selection strategies for maximizing progress from selection. The overall aim of the present study was to compare the selection progress by employing different breeding schemes and selection strategies. Two breeding schemes were considered, each involving selection in two stages: (i) developing DH lines from S0 plants and evaluating their testcrosses in stage one and testcrosses of the promising DH lines in stage two (DHTC) and (ii) early testing for testcross performance of S1 families before production of DH lines from superior S1 families and then evaluating their testcrosses in the second stage (S1TC-DHTC). For both breeding schemes, we examined different selection strategies, in which variance components and budgets varied, the cross and family structure was considered or ignored, and best linear unbiased prediction (BLUP) of testcross performance was employed. The specific objectives were to (1) maximize through optimum allocation of test resources the progress from selection, using the selection gain (ΔG) or the probability to select superior genotypes (P(q)) as well as their standard deviations as criteria, (2) investigate the effect of parental selection, varying variance components and budgets on the optimum allocation of test resources for maximizing the progress from selection, (3) assess the optimum filial generation (S0 or S1) for DH production, (4) compare various selection strategies - sequential selection considering or ignoring the cross and family structure - for maximizing progress from selection, (5) examine the effect of producing a larger number of candidates within promising crosses and S1 families on the progress from selection, and (6) determine the effect of BLUP, where information from genetically related candidates is integrated in the selection criteria, on the progress from selection. For both breeding schemes, the best strategy was to select among all S1 families and/or DH lines ignoring the cross structure. Further, in breeding scheme S1TC-DHTC, the progress from selection increased with variable sizes of crosses and S1 families, i.e., larger numbers of DH lines devoted to superior crosses and S1 families. Parental cross selection strongly influenced the optimum allocation of test resources and, consequently, the selection gain ΔG in both breeding schemes. With an increasing correlation between the mean testcross performance of the parental lines and the mean testcross performance of their progenies, the superiority in progress from selection compared to randomly chosen parents increased markedly, whereas the optimum number of parental crosses decreased in favor of an increased number of test candidates within crosses. With BLUP, information from genetically related test candidates resulted in more precise estimates of their genotypic values and the progress from selection slightly increased for both optimization criteria ΔG and P(q), compared with conventional phenotypic selection. Analytical solutions to enable fast calculations of the optimum allocation of test resources were developed. This analytical approach superseded matrix inversions required for the solution of the mixed model equations. In breeding scheme S1TC-DHTC, the optimum allocation of test resources involved (1) 10 or more test locations at both stages, (2) 10 or fewer parental crosses each with 100 to 300 S1 families at the first stage, and (3) 500 or more DH lines within a low number of parental crosses and S1 families at the second stage. In breeding scheme DHTC, the optimum number of test candidates at the first stage was 5 to 10 times larger, whereas the number of test locations at the first stage and the number of DH lines at the second stage was strongly reduced compared with S1TC-DHTC. The possibility to reduce the number of parental crosses by selection among parental lines is of utmost importance for the optimization of the allocation of test resources and maximization of the progress from selection. Further, the optimum allocation of test resources is crucial to maximize the progress from selection under given economic and quantitative-genetic parameters. By using marker information and BLUP-based genomic selection, more efficient selection strategies could be developed for hybrid maize breeding.
Stirring up sorghum hybrid breeding targeting West African smallholder farmers low input environments
(2019) Kante, Papa Ndiaga Moctar; Haussmann, Bettina
Food supply and income in rural areas of West Africa (WA) depend strongly on the local production, and mostly on farmers’ field production of root and tuber crops, and cereals. To feed an ever-increasing population in a context of climate-change and low-input cultural conditions, breeding for resilient crops can guarantee smallholder farmers food security and cash income for a sustainable rural development. Sorghum hybrids for WA were first explored in the early 1970s and hybrid crosses of Malian landraces with introduced Caudatum-race seed parents were evaluated in the early 80s. Although those hybrids exhibited good heterosis for grain yield, their lack of grain quality made them commercially unsustainable. Efforts by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) and its partners resulted in the first series of Guinea-race based hybrids. The short statured hybrids were evaluated in several on-farm farmer-managed yield trials, and showed satisfactory grain yield and quality under farmers’ cultivation conditions. Although taller- relative to shorter- height sorghum can help reduce risks of panicle loss by grazing transhumant cattle, no indication on the yield potential of the tall statured hybrids is available. The advances achieved by ICRISAT and its partners in hybrid development justified establishing a long-term hybrid breeding program to provide farmers with hybrids with sufficient grain yield and good grain quality under low input conditions. However, the lack of quantitative genetic information about the genetic value of new experimental hybrids and their parents (Guinea-Caudatum to complete Guinea background, from different WA origins), or about the efficiency of alternative selection methods for targeting yield performance in the predominantly low-input and phosphorous-deficient sorghum production conditions hinders sorghum hybrid development for this region. Sorghum hybrid breeding was commercially feasible only after the identification of a heritable and stable cytoplasmic male sterility (CMS) mechanism. Hybrid breeding in WA can benefit from molecular marker, especially for the fertility restoration/sterility maintenance of the predominant A1-type of CMS. The major outcomes of this thesis are presented as follow: Mean yields of tall hybrids were 3 to 17% (ranging from 6 to 28 g m−2) higher than that of the local check across all 37 on-farm farmer-managed environments and were highest (14–47%) averaged across the seven trials with the lowest mean yields. The yields of the new set of experimental hybrids were substantially superior to farmers’ local Guinea-race varieties, with 20 to 80% higher means over all hybrids in both low phosphorus (LP) and high phosphorus (HP) environments. Average mid-parent and better-parent heterosis estimates were respectively 78 and 48% under HP, and 75 and 42% under LP. Direct selection under LP was predicted to be 20 to 60% more effective than indirect selection under HP conditions, for hybrid performance under LP. The combining ability estimates provide initial insights into the potential benefit of germplasm from further east in West and Central Africa for developing a male parental pool that is distinct and complimentary to the Malian female pool. On chromosome SBI-05, we found a major A1 CMS fertility restorer locus (Rf5) explaining 19 and 14% of the phenotypic variation in either population. Minor quantitative trait loci (QTL) were detected in these two populations on chromosomes SBI-02, SBI-03, SBI-04 and SBI-10. In the third population, we identified one major A1 CMS fertility restorer locus on chromosome SBI-02, Rf2, explaining 31% of the phenotypic variation in the F2 mapping population. Pentatricopeptide repeat genes in the Rf2 QTL region were sequenced, and we detected in Sobic.002G057050 a missense mutation in the first exon, explaining 81% of the phenotypic variation in an F2:3 validation population and clearly separating B- from R-lines. The Guinea-race hybrids’ substantial yield superiorities over well adapted local Guinea-race varieties suggests that a strategy of breeding hybrids based on Guinea-germplasm can contribute to improving the livelihood of many smallholder farmers in WA. Although the usefulness of direct selection under LP for hybrid performance in the predominantly P-limited target environments was proven, companion evaluations of hybrids under HP would be desirable to identify also new hybrids that can respond to improved fertility conditions for sustainable intensification. The developed KASP marker stands as a promising tool for routine use in WA breeding programs.