Long-term comparison between index selection and optimal independent culling in plant breeding programs with genomic prediction

In the context of genomic selection, we evaluated and compared breeding programs using either index selection or independent culling for recurrent selection of parents. We simulated a clonally propagated crop breeding program for 20 cycles using either independent culling or an economic index with two unfavourably correlated traits under selection. Cycle time from crossing to selection of parents was kept the same for both strategies. Both methods led to increasingly unfavourable genetic correlations between traits and, compared to independent culling, index selection led to larger changes in the genetic correlation between the two traits. When linkage disequilibrium was not considered, the two methods had similar losses of genetic diversity. Two independent culling approaches were evaluated, one using optimal culling levels and one using the same selection intensity for both traits. Optimal culling levels outperformed the same selection intensity even when traits had the same economic importance. Therefore, accurately estimating optimal culling levels is essential for maximizing gains when independent culling is performed. Once optimal culling levels are achieved, independent culling and index selection lead to comparable genetic gains.

83 PENINGKATAN DAYA HASIL DAN STAY-GREEN TANAMAN JAGUNG MELALUI SELEKSI TANDEM DAN INDEPENDENT CULLING LEVEL DI LAHAN KERING

ABSTRAK Tujuan penelitian adalah untuk mengetahui kemajuan seleksi tandem dan independent culling level selama tiga siklus di lahan kering dan mengetahui rerata daya hasil dan stay-green (brangkasan segar) populasi hasil seleksi dibanding dengan populasi awal dan varietas unggul Lamuru. Percobaan dirancang dengan rancangan acak kelompok, 3 blok di lahan kering Lombok Utara. Data dianalisa dengan analisis sidik ragam pada taraf nyata 5 persen. Rata-rata kemajuan seleksi per siklus setiap cara, diperoleh dari koefisien regresi antara karakter dengan siklus seleksi (populasi). Rerata perlakuan, diuji lanjut dengan BNT0,05. Hasil penelitian menunjukkan, bahwa kemajuan seleksi per siklus kedua cara hingga siklus ketiga untuk daya hasil dan brangkasan segar bersifat linear yang nyata. Besarnya kemajuan seleksi per siklus daya hasil secara tandem dan independent culling level berturut-turut 2,19 dan 2,74 g/tan; sedangkan untuk brangkasan segar sebesar 6,86 dan 13,77 g/tan. Rerata daya hasil dan bobot brangkasan segar, populasi hasil seleksi siklus ketiga kedua cara lebih besar dibanding populasi awal. Daya hasil populasi hasil seleksi independent culling level siklus ketiga lebih besar dibanding varietas Lamuru; namun populasi hasil seleksi tandem sama. ABSTRACT The objective of this research was to determine the progress of tandem and independent culling level selections until the three cycles on dry land and determine the mean grain yield and stay - green of selected plant populations compared with the base population and Lamuru superior variety. The experiment was designed using randomized block design with 3 replicates in North Lombok dry land. The observed data were analyzed using analysis of variance and LSD at the 5 percent significance level. The average of selection progress per cycle each way was obtained from the regression coefficient between the observed characters and the selection cycle (population). The results of the research showed that the progress of selection per cycle until the third cycle for yield (dry grain seed weight) and fresh biomass for both ways were significant linear. The selection progress of yield potential for tandem selection and independent culling level were 2,19 dan 2,74 g/tan respectivelly. The selection progress of biomass weight were 6,86 dan 13,77 g/tan for tandem selection and independent culling level. Mean of yield potential and fresh biomass weight for two ways were higher base population. Yield population of independent culling level selection three cycles were higher than Lamuru variety; but population result of tandem selection as the same.

Plant breeders should be determining economic weights for a selection index instead of using independent culling for choosing parents in breeding programs with genomic selection

In the context of genomic selection, we evaluated and compared recurrent selection breeding programs using either index selection or independent culling for selection of parents. We simulated a clonally propagated crop breeding program for 20 cycles of selection using either independent culling or an economic selection index with two unfavourably correlated traits under selection. Cycle time from crossing to selection of parents was kept the same for both strategies. Our results demonstrate that accurate knowledge of the economic importance of traits is essential even when performing independent culling. This is because independent culling achieved its optimum genetic gain when the culling threshold for each trait varied accordingly to the economic importance of the traits. When gains from independent culling were maximised, the efficiency of converting genetic diversity into genetic gain of both selection methods were equivalent. When the same proportion selected of 10% for each trait was used instead of optimal culling levels, index selection was 10%, 128% and 310% more efficient than independent culling when T2 had a relative economic importance of 1.0, 2.5 and 5.0, respectively. Given the complexity of estimating optimal culling levels and the fact that the gains achieved with independent culling are, at most, equivalent to index selection, the use of an economic selection index is recommended for multi-trait genomic selection.

KERAGAMAN GENETIK IKAN MAS (Cyprinus carpio) VARIETAS RAJADANU TAHAN KOI HERPESVIRUS GENERASI F0 DAN F1 MENGGUNAKAN TIGA LOKUS MIKROSATELIT

<p>Informasi tentang keragaman genetik sangat dibutuhkan pada program pemuliaan melalui kegiatan seleksi untuk menghasilkan induk unggul, seperti pada pembentukan ikan mas Rajadanu tahan infeksi koi herpes virus (KHV). Penelitian ini bertujuan untuk mengevaluasi variasi genetik ikan mas varietas Rajadanu tahan infeksi KHV generasi F0 dan F1 dengan menggunakan marka molekuler mikrosatelit. Populasi F0 dan F1 dihasilkan dari kegiatan seleksi bersamaan (independent culling) pada karakter pertumbuhan dan ketahanan terhadap KHV. Seleksi karakter pertumbuhan dilakukan dengan metode seleksi individu (mass selection), sedangkan seleksi karakter ketahanan terhadap KHV dilakukan dengan mengidentifikasi individu yang membawa marka MHC II spesifik pada alel Cyca-DAB1*05. Sebanyak sepuluh individu ikan mas dari setiap populasi digunakan untuk analisis variabilitas mikrosatelit menggunakan tiga lokus mikrosatelit (MFW6, MFW7, dan MFW9). Data alel mikrosatelit diolah menggunakan program Microsoft excel dan dianalisis menggunakan program Fstat dan Arlequin. Hasil penelitian menunjukkan bahwa jumlah alel dari tiap lokus pada masingmasing populasi bervariasi, yaitu berkisar antara 2-5 alel. Rata-rata jumlah alel dan rata-rata heterozigositas teramati pada populasi F0 tidak berbeda dengan populasi F1. Rata-rata jumlah alel pada kedua populasi sebesar 3,33 alel dengan rata-rata nilai heterozigositas teramati sebesar 0,47. Inbreeding teridentifikasi pada populasi F0 dan F1, kedua populasi mempunyai tingkat inbreeding yang relatif sama. Populasi ikan mas tahan KHV pada penelitian ini memiliki keragaman genetik yang relatif rendah sehingga diperlukan monitoring variasi genetik dan skema pemijahan yang baik pada kegiatan seleksi selanjutnya untuk menghasilkan ikan mas tahan KHV yang unggul.</p><p>Information on genetic diversity is needed in breeding program through selective breeding to produce superior broodstocks, such as on production of Rajadanu strain of common carp resistant to KHV infection. The aim of this study was to evaluate the genetic variation in F0 and F1 of Rajadanu strain of common carp resistant to KHV infection using microsatellite marker. The F0 and F1 populations have been produced by independent culling method on growth and resistant to KHV characters. Selection on growth character was conducted by mass selection method, while selection on resistant to KHV character was conducted by identification the individual of common carp that carrying MHC II marker specific on CycaDAB1*05 allele. Ten individuals representing each population were analyzed for microsatellite variability using three microsatellite loci (MFW6, MFW7, and MFW9). Microsatellite allele data were analyzed using Microsoft Excel, Fstat, and Arlequin software. The result showed that the number of alleles per loci in each population varied ranging from 2 to 5 alleles. The average number of alleles and the average observed heterozygosity in F0 was similar to that of F1. The average number of alleles in both populations was 3.33, while the average observed heterezygosity was 0.47. The F0 and F1 populations showed inbreeding level; inbreeding level in both populations was relatively similar. Common carp populations in this study had relatively low genetic variation, so that monitoring of genetic variation and good spawning scheme were needed on next selection program to produce a superior common carp resistant to KHV.</p>

Selection Approaches in High-Elevation Coastal Douglas-fir in The Presence of GxE Interactions

Regeneration obligations in British Columbia for high-elevation coastal sites requires a secure seed supply of quality seed in coastal Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco). Consequently, a seed orchard is under development to supply seed after genetic testing and selection. For this purpose, 55 coastal Douglas-fir families were field-tested for 11 years on two contrasting high-elevation sites to examine differential growth performance and tolerance to cold conditions. Although heritabilities for growth on both sites were moderate at age 11, the higher elevation colder site had substantially slower growth and over 90% of the trees exhibited some form of cold damage to foliage, branches and stems; however, variation in this damage was not significant at the family level. Combined site analysis revealed a highly significant genotype by environment (GxE) component in height that could not be removed or reduced by using site-specific error variances or spatial analysis (i.e., GxE was primarily due to rank changes of families across the two sites). This was also reflected by a drop in heritability estimates obtained from the combined site analyses. In the presence of this type of GxE, independent culling, considering height a separate trait on each site, was employed to identify parents that were at a threshold breeding value of 5% or greater in growth superiority on both sites. Average breeding values for the selected parents, based on a combined site analysis, were around 5% above the trial mean for height at age 11. The use of independent culling, for situations where accurate genetic parameters are difficult to obtain, should be considered a practical alternative to more complex and error prone methods of selection.

Plant Breeders' Perspectives on Improving Yield and Quality Traits in Horticultural Food Crops

Breeders of horticultural food crops are usually concerned with multiple traits related to yield and quality as well as other traits such as biotic and abiotic stresses. Yield in these crops is not solely tonnage of biomass produced in the field. Rather, it is the proportion of the crop that can be harvested and brought to market in a condition and at a price acceptable to the consumer. Quality may include flavor, color, shape, size, degree of damage, nutrient levels, and traits that permit greater perceived food safety or environmental sustainability. Some traits may exhibit phenotypic associations. Traits with unfavorable associations will be of concern to the breeder if the cause is unfavorably correlated genetic effects, especially those resulting from pleiotropy. Several multiple trait selection schemes have been developed, including independent culling levels, tandem selection, and index selection. These schemes can result in improvement even for traits with unfavorable associations. However, the breeder must have a strong rationale for each trait addressed in a breeding program because each additional trait necessitates larger breeding populations and more resources. Thus, the breeder's first challenge for each crop is to determine which traits are most important and which issues are most amenable to a breeding solution.